Files in eahrne/SafeQuant
A Toolbox for the Analysis of Proteomics Data

.gitignore
DESCRIPTION
NAMESPACE
R/DIA.R R/ExpressionAnalysis.R R/GGGraphics.R R/Graphics.R R/IdentificationAnalysis.R R/Parser.R R/SafeQuantAnalysis.R R/TMT.R R/Targeted.R R/UserOptions.R R/data.R README.md
_config.yml
data/kinaseMotif.rda
exec/filterLargeProgenesisPeptideFile.pl
exec/installDependencies.R exec/roxygenize.R exec/safeQuant.R inst/manuals/SafeQuant-man.pdf
inst/manuals/SafeQuant_UseCases.txt
inst/manuals/tsv_spreadsheet_help.docx
inst/manuals/tsv_spreadsheet_help.pdf man/COLORS.Rd man/addIdQvalues.Rd man/addScaffoldPTMFAnnotations.Rd man/barplotMSSignal.Rd man/createExpDesign.Rd man/createExpressionDataset.Rd man/createPairedExpDesign.Rd man/cvBoxplot.Rd man/cysteinFreqBarplot.Rd man/dotProduct.Rd man/expDesignTagToExpDesign.Rd man/export.Rd man/getAAProteinCoordinates.Rd man/getAccessionNumber.Rd man/getAllCV.Rd man/getAllDotProduct.Rd man/getAllEBayes.Rd man/getBaselineIntensity.Rd man/getCV.Rd man/getExpDesignProgenesisCsv.Rd man/getFTestPValue.Rd man/getGeneName.Rd man/getGlobalNormFactors.Rd man/getGoTermDF.Rd man/getIBAQEset.Rd man/getIdLevelQvals.Rd man/getImpuritiesMatrix.Rd man/getImputationMatrix.Rd man/getIntSumPerProtein.Rd man/getKinaseFreq.Rd man/getKinases.Rd man/getLOD.Rd man/getLoocvFoldError.Rd man/getMaxIndex.Rd man/getMeanCenteredRange.Rd man/getModifProteinCoordinates.Rd man/getMotifFreq.Rd man/getMotifX.Rd man/getNAFraction.Rd man/getNbDetectablePeptides.Rd man/getNbMisCleavages.Rd man/getNbPeptidesPerProtein.Rd man/getNbRolledUpFeatures.Rd man/getNbSpectraPerProtein.Rd man/getPeptides.Rd man/getRTNormFactors.Rd man/getRatios.Rd man/getScoreCutOff.Rd man/getSignalPerCondition.Rd man/getSwaths.Rd man/getTopX.Rd man/getUserOptions.Rd man/ggDilutionCurve.Rd man/ggVolcanoPlot.Rd man/globalNormalize.Rd man/hClustHeatMap.Rd man/isCon.Rd man/isDecoy.Rd man/isStrippedACs.Rd man/kinaseMotif.Rd man/maPlotSQ.Rd man/missinValueBarplot.Rd man/option_list.Rd man/pairsAnnot.Rd man/parseMaxQuantProteinGroupTxt.Rd man/parseProgenesisFeatureCsv.Rd man/parseProgenesisPeptideMeasurementCsv.Rd man/parseProgenesisProteinCsv.Rd man/parseScaffoldPTMReport.Rd man/parseScaffoldRawFile.Rd man/perFeatureNormalization.Rd man/plotAbsEstCalibrationCurve.Rd man/plotAdjustedVsNonAdjustedRatio.Rd man/plotAllGGVolcanoes.Rd man/plotExpDesign.Rd man/plotIdScoreVsFDR.Rd man/plotLogo.Rd man/plotMSSignalDistributions.Rd man/plotNbIdentificationsVsRT.Rd man/plotNbValidDeFeaturesPerFDR.Rd man/plotPrecMassErrorDistrib.Rd man/plotPrecMassErrorVsScore.Rd man/plotQValueVsPValue.Rd man/plotROC.Rd man/plotRTNorm.Rd man/plotRTNormSummary.Rd man/plotScoreDistrib.Rd man/plotVolcano.Rd man/plotXYDensity.Rd man/purityCorrectTMT.Rd man/removeOutliers.Rd man/rollUp.Rd man/rollUpDT.Rd man/rtNormalize.Rd man/safeQuantAnalysis.Rd man/setNbPeptidesPerProtein.Rd man/setNbSpectraPerProtein.Rd man/sqImpute.Rd man/sqNormalize.Rd man/stripACs.Rd tests/initTestSession.R tests/runAllTest.R tests/testDIA.R
tests/testData/maxquant_protein_groups.csv
tests/testData/motifs.xls
tests/testData/mouse_proteins.fasta
tests/testData/progenesis_feature_export1.csv
tests/testData/progenesis_pep_measurement1.csv
tests/testData/progenesis_pep_measurement_fractionated1.csv
tests/testData/progenesis_protein_export1.csv
tests/testData/scaffoldPtm_spectrum_report.xls
tests/testData/scaffold_tmt10plex_calibMix_raw.xls
tests/testData/scaffold_tmt10plex_raw.xls
tests/testData/scaffold_tmt10plex_raw_phospho.xls
tests/testData/scaffold_tmt6plex_raw.xls
tests/testData/skyline_transition_results.csv
tests/testExpressionAnalysis.R tests/testGGGraphics.R tests/testGraphics.R tests/testIdentificationAnalysis.R tests/testParser.R tests/testSafeQuantAnalysis.R tests/testTMT.R tests/testTargeted.R tests/testUserOptions.R tests/test_call_rmarkdown.Rmd
tests/test_call_rmarkdown.html
eahrne/SafeQuant documentation built on Dec. 4, 2017, 4:20 p.m.